From 834a3ec2c2c2f8dd8635a4ec64865e35873ab9f1 Mon Sep 17 00:00:00 2001
From: Pedro Martinez Mediano <pedro.martinez-mediano13@imperial.ac.uk>
Date: Thu, 1 Jun 2017 17:22:42 +1000
Subject: [PATCH] Relocated GPU code and modified build and load paths
 accordingly.

---
 build.xml                                     | 24 ++++------
 .../kraskov/cuda => cuda}/FindJNI.mk          |  0
 .../continuous/kraskov/cuda => cuda}/Makefile | 44 +++++++++++--------
 .../kraskov/cuda => cuda}/benchmark.sh        |  0
 .../continuous/kraskov/cuda => cuda}/ctimer.h |  0
 .../kraskov/cuda => cuda}/cub/LICENSE.TXT     |  0
 .../kraskov/cuda => cuda}/cub/README.md       |  0
 .../kraskov/cuda => cuda}/cub/common.mk       |  0
 .../cub/cub/agent/agent_histogram.cuh         |  0
 .../cub/agent/agent_radix_sort_downsweep.cuh  |  0
 .../cub/agent/agent_radix_sort_upsweep.cuh    |  0
 .../cub/cub/agent/agent_reduce.cuh            |  0
 .../cub/cub/agent/agent_reduce_by_key.cuh     |  0
 .../cuda => cuda}/cub/cub/agent/agent_rle.cuh |  0
 .../cub/cub/agent/agent_scan.cuh              |  0
 .../cub/cub/agent/agent_segment_fixup.cuh     |  0
 .../cub/cub/agent/agent_select_if.cuh         |  0
 .../cub/cub/agent/agent_spmv_csrt.cuh         |  0
 .../cub/cub/agent/agent_spmv_orig.cuh         |  0
 .../cub/cub/agent/agent_spmv_row_based.cuh    |  0
 .../cub/agent/single_pass_scan_operators.cuh  |  0
 .../cub/block/block_adjacent_difference.cuh   |  0
 .../cub/cub/block/block_discontinuity.cuh     |  0
 .../cub/cub/block/block_exchange.cuh          |  0
 .../cub/cub/block/block_histogram.cuh         |  0
 .../cub/cub/block/block_load.cuh              |  0
 .../cub/cub/block/block_radix_rank.cuh        |  0
 .../cub/cub/block/block_radix_sort.cuh        |  0
 .../cub/cub/block/block_raking_layout.cuh     |  0
 .../cub/cub/block/block_reduce.cuh            |  0
 .../cub/cub/block/block_scan.cuh              |  0
 .../cub/cub/block/block_shuffle.cuh           |  0
 .../cub/cub/block/block_store.cuh             |  0
 .../block_histogram_atomic.cuh                |  0
 .../specializations/block_histogram_sort.cuh  |  0
 .../specializations/block_reduce_raking.cuh   |  0
 .../block_reduce_raking_commutative_only.cuh  |  0
 .../block_reduce_warp_reductions.cuh          |  0
 .../specializations/block_scan_raking.cuh     |  0
 .../specializations/block_scan_warp_scans.cuh |  0
 .../block_scan_warp_scans2.cuh                |  0
 .../block_scan_warp_scans3.cuh                |  0
 .../kraskov/cuda => cuda}/cub/cub/cub.cuh     |  0
 .../cub/cub/device/device_histogram.cuh       |  0
 .../cub/cub/device/device_partition.cuh       |  0
 .../cub/cub/device/device_radix_sort.cuh      |  0
 .../cub/cub/device/device_reduce.cuh          |  0
 .../cub/device/device_run_length_encode.cuh   |  0
 .../cub/cub/device/device_scan.cuh            |  0
 .../device/device_segmented_radix_sort.cuh    |  0
 .../cub/device/device_segmented_reduce.cuh    |  0
 .../cub/cub/device/device_select.cuh          |  0
 .../cub/cub/device/device_spmv.cuh            |  0
 .../device/dispatch/dispatch_histogram.cuh    |  0
 .../device/dispatch/dispatch_radix_sort.cuh   |  0
 .../cub/device/dispatch/dispatch_reduce.cuh   |  0
 .../dispatch/dispatch_reduce_by_key.cuh       |  0
 .../cub/cub/device/dispatch/dispatch_rle.cuh  |  0
 .../cub/cub/device/dispatch/dispatch_scan.cuh |  0
 .../device/dispatch/dispatch_select_if.cuh    |  0
 .../device/dispatch/dispatch_spmv_csrt.cuh    |  0
 .../device/dispatch/dispatch_spmv_orig.cuh    |  0
 .../dispatch/dispatch_spmv_row_based.cuh      |  0
 .../cub/cub/grid/grid_barrier.cuh             |  0
 .../cub/cub/grid/grid_even_share.cuh          |  0
 .../cub/cub/grid/grid_mapping.cuh             |  0
 .../cuda => cuda}/cub/cub/grid/grid_queue.cuh |  0
 .../cuda => cuda}/cub/cub/host/mutex.cuh      |  0
 .../cub/iterator/arg_index_input_iterator.cuh |  0
 .../cache_modified_input_iterator.cuh         |  0
 .../cache_modified_output_iterator.cuh        |  0
 .../cub/iterator/constant_input_iterator.cuh  |  0
 .../cub/iterator/counting_input_iterator.cuh  |  0
 .../cub/iterator/discard_output_iterator.cuh  |  0
 .../cub/iterator/tex_obj_input_iterator.cuh   |  0
 .../cub/iterator/tex_ref_input_iterator.cuh   |  0
 .../cub/iterator/transform_input_iterator.cuh |  0
 .../cub/cub/thread/thread_load.cuh            |  0
 .../cub/cub/thread/thread_operators.cuh       |  0
 .../cub/cub/thread/thread_reduce.cuh          |  0
 .../cub/cub/thread/thread_scan.cuh            |  0
 .../cub/cub/thread/thread_search.cuh          |  0
 .../cub/cub/thread/thread_store.cuh           |  0
 .../cuda => cuda}/cub/cub/util_allocator.cuh  |  0
 .../cuda => cuda}/cub/cub/util_arch.cuh       |  0
 .../cuda => cuda}/cub/cub/util_debug.cuh      |  0
 .../cuda => cuda}/cub/cub/util_device.cuh     |  0
 .../cuda => cuda}/cub/cub/util_macro.cuh      |  0
 .../cuda => cuda}/cub/cub/util_namespace.cuh  |  0
 .../cuda => cuda}/cub/cub/util_ptx.cuh        |  0
 .../cuda => cuda}/cub/cub/util_type.cuh       |  0
 .../warp/specializations/warp_reduce_shfl.cuh |  0
 .../warp/specializations/warp_reduce_smem.cuh |  0
 .../warp/specializations/warp_scan_shfl.cuh   |  0
 .../warp/specializations/warp_scan_smem.cuh   |  0
 .../cub/cub/warp/warp_reduce.cuh              |  0
 .../cuda => cuda}/cub/cub/warp/warp_scan.cuh  |  0
 .../kraskov/cuda => cuda}/cub/tune/.gitignore |  0
 .../kraskov/cuda => cuda}/cub/tune/Makefile   |  0
 .../cub/tune/tune_device_reduce.cu            |  0
 .../kraskov/cuda => cuda}/digamma.c           |  0
 .../kraskov/cuda => cuda}/digamma.h           |  0
 .../cuda => cuda}/findComputeCapability.cu    |  0
 .../kraskov/cuda => cuda}/gpuKnnBF_kernel.cu  |  0
 .../kraskov/cuda => cuda}/gpuKnnLibrary.c     |  0
 .../kraskov/cuda => cuda}/gpuKnnLibrary.h     |  0
 .../kraskov/cuda => cuda}/gpuMILibrary.c      |  0
 .../kraskov/cuda => cuda}/gpuMILibrary.h      |  0
 .../kraskov/cuda => cuda}/helperfunctions.cu  |  0
 .../kraskov/cuda => cuda}/kraskovCuda.c       |  0
 .../continuous/kraskov/cuda => cuda}/lest.hpp |  0
 .../kraskov/cuda => cuda}/perftest.cpp        |  0
 .../kraskov/cuda => cuda}/unittest.cpp        |  0
 ...tualInfoCalculatorMultiVariateKraskov.java |  4 +-
 114 files changed, 34 insertions(+), 38 deletions(-)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/FindJNI.mk (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/Makefile (65%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/benchmark.sh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/ctimer.h (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/LICENSE.TXT (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/README.md (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/common.mk (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_histogram.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_radix_sort_downsweep.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_radix_sort_upsweep.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_reduce_by_key.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_rle.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_segment_fixup.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_select_if.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_spmv_csrt.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_spmv_orig.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/agent_spmv_row_based.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/agent/single_pass_scan_operators.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_adjacent_difference.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_discontinuity.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_exchange.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_histogram.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_load.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_radix_rank.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_radix_sort.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_raking_layout.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_shuffle.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/block_store.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_histogram_atomic.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_histogram_sort.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_reduce_raking.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_reduce_warp_reductions.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_scan_raking.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_scan_warp_scans.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_scan_warp_scans2.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/block/specializations/block_scan_warp_scans3.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/cub.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_histogram.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_partition.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_radix_sort.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_run_length_encode.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_segmented_radix_sort.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_segmented_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_select.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/device_spmv.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_histogram.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_radix_sort.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_reduce_by_key.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_rle.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_select_if.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_spmv_csrt.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_spmv_orig.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/device/dispatch/dispatch_spmv_row_based.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/grid/grid_barrier.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/grid/grid_even_share.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/grid/grid_mapping.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/grid/grid_queue.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/host/mutex.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/arg_index_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/cache_modified_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/cache_modified_output_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/constant_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/counting_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/discard_output_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/tex_obj_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/tex_ref_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/iterator/transform_input_iterator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_load.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_operators.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_search.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/thread/thread_store.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_allocator.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_arch.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_debug.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_device.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_macro.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_namespace.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_ptx.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/util_type.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/specializations/warp_reduce_shfl.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/specializations/warp_reduce_smem.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/specializations/warp_scan_shfl.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/specializations/warp_scan_smem.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/warp_reduce.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/cub/warp/warp_scan.cuh (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/tune/.gitignore (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/tune/Makefile (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/cub/tune/tune_device_reduce.cu (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/digamma.c (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/digamma.h (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/findComputeCapability.cu (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/gpuKnnBF_kernel.cu (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/gpuKnnLibrary.c (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/gpuKnnLibrary.h (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/gpuMILibrary.c (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/gpuMILibrary.h (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/helperfunctions.cu (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/kraskovCuda.c (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/lest.hpp (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/perftest.cpp (100%)
 rename {java/source/infodynamics/measures/continuous/kraskov/cuda => cuda}/unittest.cpp (100%)

diff --git a/build.xml b/build.xml
index 728ca0b..0f6a9a1 100755
--- a/build.xml
+++ b/build.xml
@@ -12,6 +12,7 @@
 	<property name="distname" value="${mainfilename}-dist-${version}" />
 	<property name="distnamezip" value="${distname}.zip" />
 	<property name="src" location="java/source"/>
+	<property name="cudasrc" location="cuda"/>
 	<property name="bin" location="bin"/>
 	<property name="unittestsouttoplevel" location="unittests"/>
 	<property name="unittestssrc" location="java/unittests"/>
@@ -35,7 +36,9 @@
 	<!-- Make required directories -->
 	<target name="init" description="Create the compiled code directories">
 		<mkdir dir="${bin}"/>
+    <mkdir dir="${bin}/cuda"/>
 		<mkdir dir="${unittestsbin}"/>
+    <mkdir dir="${unittestsbin}/cuda"/>
 		<mkdir dir="${reports.tests}"/>
 	</target>
 
@@ -196,7 +199,7 @@
 
   <!-- Compile GPU code -->
   <target name="gpu" depends="init" description="compile only C/C++ GPU code">
-    <exec executable="make" dir="${src}/infodynamics/measures/continuous/kraskov/cuda/" resultproperty="return.code">
+    <exec executable="make" dir="${cudasrc}" failonerror="true" resultproperty="return.code">
       <env key="DEBUG" value="${DEBUG}"/>
     </exec>
     <fail>
@@ -204,18 +207,11 @@
         <isfailure code="${return.code}"/>
       </condition>
     </fail>
-    <move todir="${bin}/infodynamics/measures/continuous/kraskov/cuda">
-      <filelist dir="${src}/infodynamics/measures/continuous/kraskov/cuda">
-        <file name="gpuKnnLibrary.o"/>
-        <file name="libgpuKnnLibrary.a"/>
-        <file name="libKraskov.so"/>
-      </filelist>
-    </move>
   </target>
 
   <!-- Clean GPU code -->
   <target name="gpuclean" description="clean only C/C++ GPU code">
-    <exec executable="make" dir="${src}/infodynamics/measures/continuous/kraskov/cuda/">
+    <exec executable="make" dir="${cudasrc}" failonerror="true">
       <arg value="clean"/>
     </exec>
   </target>
@@ -224,20 +220,16 @@
   <target name="gputest" depends="gpu, compile" description="compile and run C unit tests for GPU code">
 
 		<!-- Compile and run the C-only GPU unit tests -->
-    <exec executable="make" dir="${src}/infodynamics/measures/continuous/kraskov/cuda/" resultproperty="return.code">
-      <arg value="unittest"/>
+    <exec executable="make" dir="${cudasrc}" failonerror="true" resultproperty="return.code">
+      <arg value="test"/>
     </exec>
     <fail>
       <condition>
         <isfailure code="${return.code}"/>
       </condition>
     </fail>
-    <move todir="${unittestsbin}/infodynamics/measures/continuous/kraskov/cuda"
-      file="${src}/infodynamics/measures/continuous/kraskov/cuda/unittest"/>
-    <copy todir="${unittestsbin}/infodynamics/measures/continuous/kraskov/cuda"
-      file="${bin}/infodynamics/measures/continuous/kraskov/cuda/libKraskov.so"/>
 
-    <exec executable="./unittest" dir="${unittestsbin}/infodynamics/measures/continuous/kraskov/cuda/" resultproperty="return.code"/>
+    <exec executable="./unittest" dir="${unittestsbin}/cuda/" failonerror="true" resultproperty="return.code"/>
     <fail>
       <condition>
         <isfailure code="${return.code}"/>
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/FindJNI.mk b/cuda/FindJNI.mk
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/FindJNI.mk
rename to cuda/FindJNI.mk
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/Makefile b/cuda/Makefile
similarity index 65%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/Makefile
rename to cuda/Makefile
index 0bc8341..fe920dc 100644
--- a/java/source/infodynamics/measures/continuous/kraskov/cuda/Makefile
+++ b/cuda/Makefile
@@ -13,6 +13,8 @@ NVCC       ?= nvcc
 GCC        ?= g++
 CCFLAGS    ?= -O3 -Wall -Wextra -Wno-unused-parameter
 NVCCFLAGS  ?= -O3 -D_FORCE_INLINES -Xcompiler -Wall
+BIN=../bin/cuda
+UNITBIN=../unittests/bin/cuda
 
 
 ## Quick check to find 'which' function
@@ -37,11 +39,11 @@ endif
 # COMPUTE_CAPABILITY = -arch=sm_30
 ifneq ($(MAKECMDGOALS),clean)
 ifeq (${COMPUTE_CAPABILITY},)
-  ifeq ($(wildcard findComputeCapability),)
+  ifeq ($(wildcard $(BIN)/findComputeCapability),)
     $(info Compiling diagnostics script)
-    $(shell ${NVCC} -Wno-deprecated-gpu-targets -o findComputeCapability findComputeCapability.cu)
+    $(shell ${NVCC} -Wno-deprecated-gpu-targets -o $(BIN)/findComputeCapability findComputeCapability.cu)
   endif
-  COMPUTE_CAPABILITY ?= $(shell ./findComputeCapability)
+  COMPUTE_CAPABILITY ?= $(shell $(BIN)/findComputeCapability)
   $(info CUDA compute capability found: ${COMPUTE_CAPABILITY})
 endif
 endif
@@ -72,45 +74,49 @@ endif
 
 # Common includes and paths for CUDA. This assumes the CUDA toolkit is in PATH
 INCLUDES      := -I. -I./cub -I${JNI_INCLUDE} -I${JNI_PLATFORM_INCLUDE}
-LDFLAGS       += -L. -lcuda -lcudart
+LDFLAGS       += -L. -L$(BIN) -lcuda -lcudart
+
+.PHONY: all clean test
 
 # Main target rule
-all:  libKraskov.so
+all:  $(BIN)/libKraskov.so
 
 
 ## Compile device code
 #---------------------
-gpuKnnLibrary.o: gpuKnnLibrary.c helperfunctions.cu gpuKnnBF_kernel.cu
-	${NVCC} ${NVCCFLAGS} ${INCLUDES} -x cu -Xcompiler -fPIC -c gpuKnnLibrary.c
+$(BIN)/gpuKnnLibrary.o: gpuKnnLibrary.c helperfunctions.cu gpuKnnBF_kernel.cu
+	${NVCC} ${NVCCFLAGS} ${INCLUDES} -x cu -Xcompiler -fPIC -c gpuKnnLibrary.c -o $@
 
-libgpuKnnLibrary.a: gpuKnnLibrary.o
-	${AR} -r libgpuKnnLibrary.a gpuKnnLibrary.o
+$(BIN)/libgpuKnnLibrary.a: $(BIN)/gpuKnnLibrary.o
+	${AR} -r $@ $<
 
 
 ## Compile host code
 #-------------------
-c_objects = digamma.o gpuMILibrary.o kraskovCuda.o
+# PROG=program1 program2
+# LIST=$(addprefix $(BIN)/, $(PROG))
+c_objects = $(addprefix $(BIN)/,digamma.o gpuMILibrary.o kraskovCuda.o)
 
-%.o:	%.c
+$(BIN)/%.o:	%.c
 	${GCC} ${INCLUDES} ${CCFLAGS} -x c -std=c99 -fPIC -c $< -o $@
 
 
 ## Final shared library linking
 #------------------------------
-libKraskov.so: libgpuKnnLibrary.a $(c_objects)
-	${NVCC} ${NVCCFLAGS} ${INCLUDES} -Xcompiler -fPIC -shared -o libKraskov.so $(c_objects) ${LDFLAGS} -lgpuKnnLibrary
+$(BIN)/libKraskov.so: $(BIN)/libgpuKnnLibrary.a $(c_objects)
+	${NVCC} ${NVCCFLAGS} ${INCLUDES} -Xcompiler -fPIC -shared -o $@ $(c_objects) ${LDFLAGS} -lgpuKnnLibrary
 
 
 ## Test binary targets
 #------------------------------
-test:	unittest perftest
+test:	$(UNITBIN)/unittest $(UNITBIN)/perftest
 
-unittest:	libKraskov.so unittest.cpp
-	${GCC} ${CCFLAGS} -std=c++11 unittest.cpp -L. -lKraskov -o $@ 
+$(UNITBIN)/unittest:	unittest.cpp $(BIN)/libKraskov.so
+	${GCC} ${CCFLAGS} -std=c++11 $< -Wl,-rpath,"$(abspath $(BIN))" -L$(BIN) -lKraskov -o $@ 
 
-perftest: libKraskov.so perftest.cpp 
-	${GCC} ${CCFLAGS} -DTIMER -std=c++11 perftest.cpp -L. -lKraskov -o $@ 
+$(UNITBIN)/perftest: perftest.cpp $(BIN)/libKraskov.so
+	${GCC} ${CCFLAGS} -DTIMER -std=c++11 $< -L$(BIN) -lKraskov -o $@ 
 
 clean:
-	rm -f *.o *.so *.a unittest perftest
+	rm -f $(BIN)/* $(UNITBIN)/*
 
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/benchmark.sh b/cuda/benchmark.sh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/benchmark.sh
rename to cuda/benchmark.sh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/ctimer.h b/cuda/ctimer.h
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/ctimer.h
rename to cuda/ctimer.h
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/LICENSE.TXT b/cuda/cub/LICENSE.TXT
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/LICENSE.TXT
rename to cuda/cub/LICENSE.TXT
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/README.md b/cuda/cub/README.md
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/README.md
rename to cuda/cub/README.md
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/common.mk b/cuda/cub/common.mk
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/common.mk
rename to cuda/cub/common.mk
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_histogram.cuh b/cuda/cub/cub/agent/agent_histogram.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_histogram.cuh
rename to cuda/cub/cub/agent/agent_histogram.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_radix_sort_downsweep.cuh b/cuda/cub/cub/agent/agent_radix_sort_downsweep.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_radix_sort_downsweep.cuh
rename to cuda/cub/cub/agent/agent_radix_sort_downsweep.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_radix_sort_upsweep.cuh b/cuda/cub/cub/agent/agent_radix_sort_upsweep.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_radix_sort_upsweep.cuh
rename to cuda/cub/cub/agent/agent_radix_sort_upsweep.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_reduce.cuh b/cuda/cub/cub/agent/agent_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_reduce.cuh
rename to cuda/cub/cub/agent/agent_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_reduce_by_key.cuh b/cuda/cub/cub/agent/agent_reduce_by_key.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_reduce_by_key.cuh
rename to cuda/cub/cub/agent/agent_reduce_by_key.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_rle.cuh b/cuda/cub/cub/agent/agent_rle.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_rle.cuh
rename to cuda/cub/cub/agent/agent_rle.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_scan.cuh b/cuda/cub/cub/agent/agent_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_scan.cuh
rename to cuda/cub/cub/agent/agent_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_segment_fixup.cuh b/cuda/cub/cub/agent/agent_segment_fixup.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_segment_fixup.cuh
rename to cuda/cub/cub/agent/agent_segment_fixup.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_select_if.cuh b/cuda/cub/cub/agent/agent_select_if.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_select_if.cuh
rename to cuda/cub/cub/agent/agent_select_if.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_csrt.cuh b/cuda/cub/cub/agent/agent_spmv_csrt.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_csrt.cuh
rename to cuda/cub/cub/agent/agent_spmv_csrt.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_orig.cuh b/cuda/cub/cub/agent/agent_spmv_orig.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_orig.cuh
rename to cuda/cub/cub/agent/agent_spmv_orig.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_row_based.cuh b/cuda/cub/cub/agent/agent_spmv_row_based.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/agent_spmv_row_based.cuh
rename to cuda/cub/cub/agent/agent_spmv_row_based.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/single_pass_scan_operators.cuh b/cuda/cub/cub/agent/single_pass_scan_operators.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/agent/single_pass_scan_operators.cuh
rename to cuda/cub/cub/agent/single_pass_scan_operators.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_adjacent_difference.cuh b/cuda/cub/cub/block/block_adjacent_difference.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_adjacent_difference.cuh
rename to cuda/cub/cub/block/block_adjacent_difference.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_discontinuity.cuh b/cuda/cub/cub/block/block_discontinuity.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_discontinuity.cuh
rename to cuda/cub/cub/block/block_discontinuity.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_exchange.cuh b/cuda/cub/cub/block/block_exchange.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_exchange.cuh
rename to cuda/cub/cub/block/block_exchange.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_histogram.cuh b/cuda/cub/cub/block/block_histogram.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_histogram.cuh
rename to cuda/cub/cub/block/block_histogram.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_load.cuh b/cuda/cub/cub/block/block_load.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_load.cuh
rename to cuda/cub/cub/block/block_load.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_radix_rank.cuh b/cuda/cub/cub/block/block_radix_rank.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_radix_rank.cuh
rename to cuda/cub/cub/block/block_radix_rank.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_radix_sort.cuh b/cuda/cub/cub/block/block_radix_sort.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_radix_sort.cuh
rename to cuda/cub/cub/block/block_radix_sort.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_raking_layout.cuh b/cuda/cub/cub/block/block_raking_layout.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_raking_layout.cuh
rename to cuda/cub/cub/block/block_raking_layout.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_reduce.cuh b/cuda/cub/cub/block/block_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_reduce.cuh
rename to cuda/cub/cub/block/block_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_scan.cuh b/cuda/cub/cub/block/block_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_scan.cuh
rename to cuda/cub/cub/block/block_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_shuffle.cuh b/cuda/cub/cub/block/block_shuffle.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_shuffle.cuh
rename to cuda/cub/cub/block/block_shuffle.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_store.cuh b/cuda/cub/cub/block/block_store.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/block_store.cuh
rename to cuda/cub/cub/block/block_store.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_histogram_atomic.cuh b/cuda/cub/cub/block/specializations/block_histogram_atomic.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_histogram_atomic.cuh
rename to cuda/cub/cub/block/specializations/block_histogram_atomic.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_histogram_sort.cuh b/cuda/cub/cub/block/specializations/block_histogram_sort.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_histogram_sort.cuh
rename to cuda/cub/cub/block/specializations/block_histogram_sort.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_raking.cuh b/cuda/cub/cub/block/specializations/block_reduce_raking.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_raking.cuh
rename to cuda/cub/cub/block/specializations/block_reduce_raking.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh b/cuda/cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh
rename to cuda/cub/cub/block/specializations/block_reduce_raking_commutative_only.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_warp_reductions.cuh b/cuda/cub/cub/block/specializations/block_reduce_warp_reductions.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_reduce_warp_reductions.cuh
rename to cuda/cub/cub/block/specializations/block_reduce_warp_reductions.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_raking.cuh b/cuda/cub/cub/block/specializations/block_scan_raking.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_raking.cuh
rename to cuda/cub/cub/block/specializations/block_scan_raking.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans.cuh b/cuda/cub/cub/block/specializations/block_scan_warp_scans.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans.cuh
rename to cuda/cub/cub/block/specializations/block_scan_warp_scans.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans2.cuh b/cuda/cub/cub/block/specializations/block_scan_warp_scans2.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans2.cuh
rename to cuda/cub/cub/block/specializations/block_scan_warp_scans2.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans3.cuh b/cuda/cub/cub/block/specializations/block_scan_warp_scans3.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/block/specializations/block_scan_warp_scans3.cuh
rename to cuda/cub/cub/block/specializations/block_scan_warp_scans3.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/cub.cuh b/cuda/cub/cub/cub.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/cub.cuh
rename to cuda/cub/cub/cub.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_histogram.cuh b/cuda/cub/cub/device/device_histogram.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_histogram.cuh
rename to cuda/cub/cub/device/device_histogram.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_partition.cuh b/cuda/cub/cub/device/device_partition.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_partition.cuh
rename to cuda/cub/cub/device/device_partition.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_radix_sort.cuh b/cuda/cub/cub/device/device_radix_sort.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_radix_sort.cuh
rename to cuda/cub/cub/device/device_radix_sort.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_reduce.cuh b/cuda/cub/cub/device/device_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_reduce.cuh
rename to cuda/cub/cub/device/device_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_run_length_encode.cuh b/cuda/cub/cub/device/device_run_length_encode.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_run_length_encode.cuh
rename to cuda/cub/cub/device/device_run_length_encode.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_scan.cuh b/cuda/cub/cub/device/device_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_scan.cuh
rename to cuda/cub/cub/device/device_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_segmented_radix_sort.cuh b/cuda/cub/cub/device/device_segmented_radix_sort.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_segmented_radix_sort.cuh
rename to cuda/cub/cub/device/device_segmented_radix_sort.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_segmented_reduce.cuh b/cuda/cub/cub/device/device_segmented_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_segmented_reduce.cuh
rename to cuda/cub/cub/device/device_segmented_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_select.cuh b/cuda/cub/cub/device/device_select.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_select.cuh
rename to cuda/cub/cub/device/device_select.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_spmv.cuh b/cuda/cub/cub/device/device_spmv.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/device_spmv.cuh
rename to cuda/cub/cub/device/device_spmv.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_histogram.cuh b/cuda/cub/cub/device/dispatch/dispatch_histogram.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_histogram.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_histogram.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_radix_sort.cuh b/cuda/cub/cub/device/dispatch/dispatch_radix_sort.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_radix_sort.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_radix_sort.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_reduce.cuh b/cuda/cub/cub/device/dispatch/dispatch_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_reduce.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_reduce_by_key.cuh b/cuda/cub/cub/device/dispatch/dispatch_reduce_by_key.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_reduce_by_key.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_reduce_by_key.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_rle.cuh b/cuda/cub/cub/device/dispatch/dispatch_rle.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_rle.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_rle.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_scan.cuh b/cuda/cub/cub/device/dispatch/dispatch_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_scan.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_select_if.cuh b/cuda/cub/cub/device/dispatch/dispatch_select_if.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_select_if.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_select_if.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_csrt.cuh b/cuda/cub/cub/device/dispatch/dispatch_spmv_csrt.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_csrt.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_spmv_csrt.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_orig.cuh b/cuda/cub/cub/device/dispatch/dispatch_spmv_orig.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_orig.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_spmv_orig.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_row_based.cuh b/cuda/cub/cub/device/dispatch/dispatch_spmv_row_based.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/device/dispatch/dispatch_spmv_row_based.cuh
rename to cuda/cub/cub/device/dispatch/dispatch_spmv_row_based.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_barrier.cuh b/cuda/cub/cub/grid/grid_barrier.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_barrier.cuh
rename to cuda/cub/cub/grid/grid_barrier.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_even_share.cuh b/cuda/cub/cub/grid/grid_even_share.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_even_share.cuh
rename to cuda/cub/cub/grid/grid_even_share.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_mapping.cuh b/cuda/cub/cub/grid/grid_mapping.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_mapping.cuh
rename to cuda/cub/cub/grid/grid_mapping.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_queue.cuh b/cuda/cub/cub/grid/grid_queue.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/grid/grid_queue.cuh
rename to cuda/cub/cub/grid/grid_queue.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/host/mutex.cuh b/cuda/cub/cub/host/mutex.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/host/mutex.cuh
rename to cuda/cub/cub/host/mutex.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/arg_index_input_iterator.cuh b/cuda/cub/cub/iterator/arg_index_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/arg_index_input_iterator.cuh
rename to cuda/cub/cub/iterator/arg_index_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/cache_modified_input_iterator.cuh b/cuda/cub/cub/iterator/cache_modified_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/cache_modified_input_iterator.cuh
rename to cuda/cub/cub/iterator/cache_modified_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/cache_modified_output_iterator.cuh b/cuda/cub/cub/iterator/cache_modified_output_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/cache_modified_output_iterator.cuh
rename to cuda/cub/cub/iterator/cache_modified_output_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/constant_input_iterator.cuh b/cuda/cub/cub/iterator/constant_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/constant_input_iterator.cuh
rename to cuda/cub/cub/iterator/constant_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/counting_input_iterator.cuh b/cuda/cub/cub/iterator/counting_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/counting_input_iterator.cuh
rename to cuda/cub/cub/iterator/counting_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/discard_output_iterator.cuh b/cuda/cub/cub/iterator/discard_output_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/discard_output_iterator.cuh
rename to cuda/cub/cub/iterator/discard_output_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/tex_obj_input_iterator.cuh b/cuda/cub/cub/iterator/tex_obj_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/tex_obj_input_iterator.cuh
rename to cuda/cub/cub/iterator/tex_obj_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/tex_ref_input_iterator.cuh b/cuda/cub/cub/iterator/tex_ref_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/tex_ref_input_iterator.cuh
rename to cuda/cub/cub/iterator/tex_ref_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/transform_input_iterator.cuh b/cuda/cub/cub/iterator/transform_input_iterator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/iterator/transform_input_iterator.cuh
rename to cuda/cub/cub/iterator/transform_input_iterator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_load.cuh b/cuda/cub/cub/thread/thread_load.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_load.cuh
rename to cuda/cub/cub/thread/thread_load.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_operators.cuh b/cuda/cub/cub/thread/thread_operators.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_operators.cuh
rename to cuda/cub/cub/thread/thread_operators.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_reduce.cuh b/cuda/cub/cub/thread/thread_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_reduce.cuh
rename to cuda/cub/cub/thread/thread_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_scan.cuh b/cuda/cub/cub/thread/thread_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_scan.cuh
rename to cuda/cub/cub/thread/thread_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_search.cuh b/cuda/cub/cub/thread/thread_search.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_search.cuh
rename to cuda/cub/cub/thread/thread_search.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_store.cuh b/cuda/cub/cub/thread/thread_store.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/thread/thread_store.cuh
rename to cuda/cub/cub/thread/thread_store.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_allocator.cuh b/cuda/cub/cub/util_allocator.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_allocator.cuh
rename to cuda/cub/cub/util_allocator.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_arch.cuh b/cuda/cub/cub/util_arch.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_arch.cuh
rename to cuda/cub/cub/util_arch.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_debug.cuh b/cuda/cub/cub/util_debug.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_debug.cuh
rename to cuda/cub/cub/util_debug.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_device.cuh b/cuda/cub/cub/util_device.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_device.cuh
rename to cuda/cub/cub/util_device.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_macro.cuh b/cuda/cub/cub/util_macro.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_macro.cuh
rename to cuda/cub/cub/util_macro.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_namespace.cuh b/cuda/cub/cub/util_namespace.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_namespace.cuh
rename to cuda/cub/cub/util_namespace.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_ptx.cuh b/cuda/cub/cub/util_ptx.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_ptx.cuh
rename to cuda/cub/cub/util_ptx.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_type.cuh b/cuda/cub/cub/util_type.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/util_type.cuh
rename to cuda/cub/cub/util_type.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_reduce_shfl.cuh b/cuda/cub/cub/warp/specializations/warp_reduce_shfl.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_reduce_shfl.cuh
rename to cuda/cub/cub/warp/specializations/warp_reduce_shfl.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_reduce_smem.cuh b/cuda/cub/cub/warp/specializations/warp_reduce_smem.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_reduce_smem.cuh
rename to cuda/cub/cub/warp/specializations/warp_reduce_smem.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_scan_shfl.cuh b/cuda/cub/cub/warp/specializations/warp_scan_shfl.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_scan_shfl.cuh
rename to cuda/cub/cub/warp/specializations/warp_scan_shfl.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_scan_smem.cuh b/cuda/cub/cub/warp/specializations/warp_scan_smem.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/specializations/warp_scan_smem.cuh
rename to cuda/cub/cub/warp/specializations/warp_scan_smem.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/warp_reduce.cuh b/cuda/cub/cub/warp/warp_reduce.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/warp_reduce.cuh
rename to cuda/cub/cub/warp/warp_reduce.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/warp_scan.cuh b/cuda/cub/cub/warp/warp_scan.cuh
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/cub/warp/warp_scan.cuh
rename to cuda/cub/cub/warp/warp_scan.cuh
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/.gitignore b/cuda/cub/tune/.gitignore
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/.gitignore
rename to cuda/cub/tune/.gitignore
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/Makefile b/cuda/cub/tune/Makefile
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/Makefile
rename to cuda/cub/tune/Makefile
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/tune_device_reduce.cu b/cuda/cub/tune/tune_device_reduce.cu
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/cub/tune/tune_device_reduce.cu
rename to cuda/cub/tune/tune_device_reduce.cu
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/digamma.c b/cuda/digamma.c
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/digamma.c
rename to cuda/digamma.c
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/digamma.h b/cuda/digamma.h
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/digamma.h
rename to cuda/digamma.h
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/findComputeCapability.cu b/cuda/findComputeCapability.cu
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/findComputeCapability.cu
rename to cuda/findComputeCapability.cu
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnBF_kernel.cu b/cuda/gpuKnnBF_kernel.cu
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnBF_kernel.cu
rename to cuda/gpuKnnBF_kernel.cu
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnLibrary.c b/cuda/gpuKnnLibrary.c
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnLibrary.c
rename to cuda/gpuKnnLibrary.c
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnLibrary.h b/cuda/gpuKnnLibrary.h
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/gpuKnnLibrary.h
rename to cuda/gpuKnnLibrary.h
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/gpuMILibrary.c b/cuda/gpuMILibrary.c
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/gpuMILibrary.c
rename to cuda/gpuMILibrary.c
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/gpuMILibrary.h b/cuda/gpuMILibrary.h
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/gpuMILibrary.h
rename to cuda/gpuMILibrary.h
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/helperfunctions.cu b/cuda/helperfunctions.cu
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/helperfunctions.cu
rename to cuda/helperfunctions.cu
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/kraskovCuda.c b/cuda/kraskovCuda.c
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/kraskovCuda.c
rename to cuda/kraskovCuda.c
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/lest.hpp b/cuda/lest.hpp
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/lest.hpp
rename to cuda/lest.hpp
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/perftest.cpp b/cuda/perftest.cpp
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/perftest.cpp
rename to cuda/perftest.cpp
diff --git a/java/source/infodynamics/measures/continuous/kraskov/cuda/unittest.cpp b/cuda/unittest.cpp
similarity index 100%
rename from java/source/infodynamics/measures/continuous/kraskov/cuda/unittest.cpp
rename to cuda/unittest.cpp
diff --git a/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java b/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
index 91dbb94..c83abfe 100755
--- a/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
+++ b/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
@@ -717,9 +717,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
         }
         String jarFolder = jarPath.toString().substring(0, jarPath.toString().lastIndexOf(fileSep));
         String relPath = fileSep + "bin" + fileSep +
-                        "infodynamics" + fileSep + "measures" + fileSep +
-                        "continuous" + fileSep + "kraskov" + fileSep + "cuda" +
-                        fileSep + "libKraskov.so";
+                        "cuda" + fileSep + "libKraskov.so";
         fullPath = jarFolder + relPath;
       } else {
         // Otherwise, use the provided path.